The airline also announced today it will halt flights between November and March from Edinburgh to Szczecin in Poland and Hamburg, and Glasgow to Las Palmas in the Canaries.
These total some 50 flights a week - or around 1,000 over the winter.
They are among 18,000 flights cancellations on 34 routes which will affect 400,000 passengers.
These have been ordered as Ryanair grounds 25 aircraft for the winter in an attempt to solve the pilot shortage.
It has already cancelled some 30 flights from the Scottish airports last week among some 2,000 across its European network until October.
Ryanair said the cutbacks would enable it to “roster all of the extra pilot leave necessary”.
The airline flies up to six times a day between Edinburgh and Stansted, and three times a day from Glasgow.
The Szczecin and Hamburg flights were due to operate twice a week, and the Las Palmas flights once a week
The cancellations start from Sunday 29 October.
Aviation analyst John Strickland, of JLS Consulting, said there could be a big loss for the airline from suspending the Stansted routes, on which it competes with EasyJet.
He told The Scotsman: “Ryanair appears to be taking additional measures to make absolutely certain they avoid any repeat of the current problems.
“Certainly, the Edinburgh and Glasgow routes are ones in which they have invested capacity and which should be strong winter performers for business traffic.
“They may be deemed a reluctant but necessary sacrifice for the objectives of restoring broader network wide reliability.”
Ryanair chief executive Michael O’Leary has blamed the move on mismanagement of pilots’ annual leave, leading to the over-allocation of blocks of holidays.
The flight cancellations have so far cost the airline around £22 million.
Ryanair said the latest step would “eliminate all risk of further flight cancellations” and remove the risk of similar problems recurring next year.
The firm also plans cut-price ticket sales this winter because it is “confident there will be no further roster related cancellations”.
It said all affected passengers had received an email alerting them and offering alternative flights or full refunds.
They have also received a £35 (€40) travel voucher.
Alex Neill, managing director of consumer group Which? Home and Product Services, said: “This situation is a complete and utter shambles that now extends to up to nearly three quarters of a million people.
“The news means that for some of its passengers Ryanair has effectively cancelled Christmas.
“On top of leaving the travel plans of many in tatters, offering a €40 voucher will be cold comfort for passengers that can’t book the flight they need.”
A Glasgow Airport spokesman said: “Today’s announcement is clearly disappointing, however, we expect these services to resume in March next year and tickets are currently on sale.”
Mr O’Leary said: “We sincerely apologise to those customers who have been affected by last week’s flight cancellations, or these sensible schedule changes announced today.
“From today, there will be no more rostering-related flight cancellations this winter or in summer 2018.
“Slower growth this winter will create lots of spare aircraft and crews which will allow us to manage the exceptional volumes of annual leave we committed to delivering in the nine months to December 2017.
“We will start a new 12 month leave period on the 1 January 2018 in full compliance with EU regulations and the Irish Aviation Authority’s requirements.”